I'd say his biggest blunder was that God awful Gravity arc.
And having T'challa pwnn the surfer.
The Gravity situation was not entirely his fault. Originally, the idea was to have Gravity sacrifice himself in the mini series BEYOND! and to return as a new Captain Marvel. However, while BEYOND! was coming out and so on, the editorial board decided to seemingly bring back THE Captain Marvel (as chronicled in CW: THE RETURN and the Reed/Weeks CAPTAIN MARVEL mini). This left McDuffie with a seemingly deceased Gravity with the Watcher claiming it was "only a beginning".
He could have gone the Bendis route, which would have been to shrug his narrative shoulders and go, "**** Gravity, that's someone else's problem now. How about some ninjas and dinosaurs!" Instead he made reviving Gravity to his proper power level a priority. Maybe involving him as a short lived cosmic level hero was a complicated way to do it, but I thought it was a decent bit of experience for the hero. He was revived, got back to his power level and even seemingly had Watcher return his secret identity status (somehow) for helping Dr. Strange and the Fantastic Four save Eternity.
In fact, the biggest caveat to that story also involved a woman. McDuffie had Gravity reveal his identity to his college girlfriend from the original McKeever mini, and she was there for his funeral. Gravity returned and simply stayed in his home state with his parents rather than at least drop a line on panel to his heartsick girlfriend, which stands as a bit cad-ish.
And yes, Black Panther outwrestling Silver Surfer was rather weak. But he's been trying to rival Batman's ridiculous "Prep Time" gimmick for a few years now.
But, after that space arc, what was next? Generic conflicts between the Frightful Four and an alternate timeline incarnation of Doom and the Four. I was far more interested in the Gravity stuff. McDuffie didn't handle him perfectly, but he'd have been in limbo just like The Loners without him. At least now he's part of The Initiative (the Nevada team, I believe).
I kinda wish we got to see the black panther and Storm stay on the FF for a lil while longer, i feel like there was a lot of potential that we never got to see with that "new" FF.
I don't know about that. While the Fantastic Four seem obligated to mix up their roster at least once a decade for about a year or so, they never last and are almost intentionally utilized as gimmicks. I wasn't sold on it originally, but McDuffie had Storm and Black Panther have a few moments, but I don't miss them either.
The one superhero who should have joined the team officially in some fashion is, of course, Spider-Man. He's been connected to the team since ASM #1 and they were connected franchises for decades after. Every time Peter had a superhero crisis, the Four were on speed-dial. He and Johnny were teenage rivals. But instead, he decides to latch onto Iron Man and join the Avengers, who he never liked enough to even remain on a reserve roster before. Makes total sense, right?
That's all my opinion, of course. But Dan Slott's SPIDER-MAN/HUMAN TORCH and Jeff Parker's SPIDER-MAN & THE FANTASTIC FOUR ('Ringo's last mini) imply I'm not alone. If Spidey had to have joined any team, continuity wise the Four made the most sense. But, of course, in 2004, probably the biggest editorial demand for Bendis' new Avengers roster was "Wolverine and Spider-Man have to be on it", so that's all moot.